AMBER: Poisson Boltzmann dynamics error

From: Rachel Burdge <rlburdge.artsci.wustl.edu>
Date: Thu, 10 Feb 2005 10:04:55 -0600

Amber users,

I am trying to run MD of a 53,059 atom system with a restraint on part
of the protein. I solvated using a cap around the area of interest, and
tried to run MD using igb = 10, which calculates a reaction field for
the system, and the run crashes. Alternatively, this same system works
fine with Generalized Born (igb = 1).

I get the following error with igb = 10:

4. RESULTS
--------------------------------------------------------------------------------
 PB bomb in pb_reslist(): maxnbr too small


According to a previous post, this error could be fixed by increasing
the cutres. When I add "cutres" to the input file to increase it from
the default of 12 to a value of 15, the run immediately crashes and I
get the following error:

PGFIO-F-239/namelist read/unit=5/entity name is not member of group.
 File name = initialMD.in formatted, sequential access record = 11
 In source file _mdread.f, at line number 1088

Has anyone experienced a similar error?

Thank you!
Rachel Burdge
Washington University in St. Louis


Here is my complete output file:
 -------------------------------------------------------
          Amber 8 SANDER Scripps/UCSF 2004
          -------------------------------------------------------
                                                                                
| Run on 02/10/2005 at 09:54:55
  [-O]verwriting output
                                                                                
File Assignments:
| MDIN: initialMD.in
| MDOUT: initialMD.out
|INPCRD: start.crd
| PARM: start.top
|RESTRT: restrt
| REFC: start.crd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: initialMD.info
|INPDIP: inpdip
|RSTDIP: rstdip
                                                                                
                                                                                
 Here is the input file:
                                                                                
MD of solvent only, 50K, 10ps, 1fs step, no shake, npt
 &cntrl
                                                                                
  nmropt = 0,
  ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
  ntpr = 50, ntwx = 500, ntwv = 0, ntwe = 0,
                                                                                
  ntf = 1, ntb = 0,
  cut = 40.0, nsnb = 10,
                                                                                
  ibelly = 0, ntr = 1, igb = 10,
                                                                                
  restraintmask = ':* & !:2855<:20.0 & !:WAT',
  restraint_wt = 10,
                                                                                
  imin = 0,
  nstlim = 10000,
  nscm = 0,
  t = 0.0, dt = 0.001,
                                                                                
  temp0 = 50.0, tempi = 50.0,
                                                                                
  ig = 71277, heat = 0.0,
  ntt = 1,
  tautp = 0.2,
  vrand = 50,
  vlimit = 15.0,
                                                                                
  ntp = 0, pres0 = 1.0, comp = 44.6,
  taup = 0.2, npscal = 1,
ntc = 1, tol = 0.00001,
                                                                                
 &end
                                                                                
                                                                                
-------------------------------------------------------------------------------- 1. RESOURCE USE:
--------------------------------------------------------------------------------
                                                                                
Warning: heat has been retired.
  Check the Retired Namelist Variables Appendix in the manual.
                                                                                
| Flags: MPI
| New format PARM file being parsed.
| Version = 1.000 Date = 02/08/05 Time = 13:16:17
 NATOM = 53059 NTYPES = 19 NBONH = 29806 MBONA = 23838
 NTHETH = 51387 MTHETA = 32519 NPHIH = 96811 MPHIA = 60226
 NHPARM = 0 NPARM = 0 NNB = 262835 NRES = 5254
 NBONA = 23838 NTHETA = 32519 NPHIA = 60226 NUMBND = 74
 NUMANG = 166 NPTRA = 66 NATYP = 39 NPHB = 1
 IFBOX = 0 NMXRS = 33 IFCAP = 1 NEXTRA = 0
 NCOPY = 0
                                                                                
                                                                                
| Memory Use Allocated
| Real 1699784
| Hollerith 323610
| Integer 2475577
| Max Pairs 1
| Max Rstack 1
| Max Istack 1
| Total 24213 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
-------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
                                                                                
                                                                                
General flags:
     imin = 0, nmropt = 0
                                                                                
Nature and format of input:
     ntx = 1, irest = 0, ntrx = 1
                                                                                
Nature and format of output:
     ntxo = 1, ntpr = 50, ntrx = 1, ntwr
= 500
     iwrap = 0, ntwx = 500, ntwv = 0, ntwe
= 0
     ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
                                                                                
Potential function:
     ntf = 1, ntb = 0, igb = 10, nsnb
= 10
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 40.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000
                                                                                
Frozen or restrained atoms:
     ibelly = 0, ntr = 1
                                                                                
Molecular dynamics:
     nstlim = 10000, nscm = 9999999, nrespa = 1
     t = 0.00000, dt = 0.00100, vlimit = 15.00000
                                                                                
Berendsen (weak-coupling) temperature regulation:
     temp0 = 50.00000, tempi = 50.00000, tautp = 0.20000
                                                                                
Water cap:
     ivcap = 0, natcap = 45862
     fcap = 1.50000, cutcap = 50.00000
     xcap = 76.00000, ycap = 93.00000, zcap = 44.00000
                                                                                
    LOADING THE CONSTRAINED ATOMS AS GROUPS
                                                                                
                                                                                
   5. REFERENCE ATOM COORDINATES
                                                                                
                                                                                
     Mask :* & !:2855<:20.0 & !:WAT; matches 40729 atoms
                                                                                
-------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
                                                                                
 begin time read from input coords = 0.000 ps
                                                                                
 Number of triangulated 3-point waters found: 2399
| Atom division among processors:
| 0 26534 53059
| Running AMBER/MPI version on 2 nodes
                                                                                
                                                                                
-------------------------------------------------------------------------------- 4. RESULTS
--------------------------------------------------------------------------------
 PB bomb in pb_reslist(): maxnbr too small
(END)





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Received on Thu Feb 10 2005 - 16:53:00 PST
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